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Detailed information for vg0402252227:

Variant ID: vg0402252227 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2252227
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


GACCATGCACGTCATTGGCACCGCAATGTCATCGCCTACCCCGGCAACCACTATCCTTCGCCTGGAACACCACCTCCCGTGATGCCTCTCCCTCTGCCTC[A/G]
CCAGCACTTCCTCTGGTAGCCATTGCAACCTCGCAGAACACCGCCCCGTTACGCAACCACCACTCAAAAACGTAGAGGCGTTCTCCTCCCCGGTCTCGCT

Reverse complement sequence

AGCGAGACCGGGGAGGAGAACGCCTCTACGTTTTTGAGTGGTGGTTGCGTAACGGGGCGGTGTTCTGCGAGGTTGCAATGGCTACCAGAGGAAGTGCTGG[T/C]
GAGGCAGAGGGAGAGGCATCACGGGAGGTGGTGTTCCAGGCGAAGGATAGTGGTTGCCGGGGTAGGCGATGACATTGCGGTGCCAATGACGTGCATGGTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.70% 18.90% 1.12% 24.31% NA
All Indica  2759 75.80% 1.80% 1.49% 20.99% NA
All Japonica  1512 16.10% 53.30% 0.60% 29.96% NA
Aus  269 81.40% 2.20% 0.74% 15.61% NA
Indica I  595 93.40% 0.80% 0.67% 5.04% NA
Indica II  465 96.60% 1.30% 0.43% 1.72% NA
Indica III  913 57.80% 1.20% 1.20% 39.76% NA
Indica Intermediate  786 70.90% 3.40% 3.05% 22.65% NA
Temperate Japonica  767 1.60% 86.80% 0.39% 11.21% NA
Tropical Japonica  504 41.50% 16.70% 0.79% 41.07% NA
Japonica Intermediate  241 9.50% 23.20% 0.83% 66.39% NA
VI/Aromatic  96 25.00% 9.40% 0.00% 65.62% NA
Intermediate  90 62.20% 23.30% 1.11% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402252227 A -> DEL LOC_Os04g04670.1 N frameshift_variant Average:68.117; most accessible tissue: Zhenshan97 young leaf, score: 91.232 N N N N
vg0402252227 A -> G LOC_Os04g04670.1 synonymous_variant ; p.Gly8Gly; LOW synonymous_codon Average:68.117; most accessible tissue: Zhenshan97 young leaf, score: 91.232 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402252227 NA 1.04E-12 mr1010 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 9.23E-06 9.23E-06 mr1261 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 5.56E-06 NA mr1392 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 1.21E-06 NA mr1546 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 NA 1.51E-06 mr1546 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 NA 7.88E-07 mr1627 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 NA 3.50E-09 mr1663 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 NA 9.77E-07 mr1785 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 NA 1.78E-09 mr1977 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 NA 2.58E-06 mr1977 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0402252227 NA 3.35E-07 mr1837_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251